Amino Acids & Proteins: Structure & Terms

CHEAmino Acids & Proteins

$\alpha$ -Amino acids are the monomers of proteins and behave as internal acid-base salts (zwitterions), explaining their physical properties. This subtopic tests definitions (zwitterion, isoelectric point, peptide bond, essential amino acid) and the acidic/basic/neutral classification.

General

\alpha

-amino acid

H_2N\text{-}\underset{\underset{R}{|}}{CH}\text{-}COOH

Both

\text{-}NH_2

and

\text{-}COOH

are on the

\alpha

-carbon; side chain

R

sets the class.

Zwitterion equilibrium

H_2N\text{-}CHR\text{-}COOH \rightleftharpoons {}^+H_3N\text{-}CHR\text{-}COO^-

Internal proton transfer gives the dipolar (zwitterionic) form that predominates in the solid and at the

pI

Peptide-bond formation

\text{-}COOH + H_2N\text{-} \rightarrow \text{-}CO\text{-}NH\text{-} + H_2O

Amide (peptide) linkage between two amino acids with loss of water.

An $\alpha$ -amino acid has $\text{-}NH_2$ and $\text{-}COOH$ on the same carbon: general form $H_2N\text{-}CHR\text{-}COOH$ ; the side chain R sets its class and properties.
A zwitterion is the dipolar form $H_3N^+\text{-}CHR\text{-}COO^-$ in which the $\text{-}COOH$ has donated a proton to $\text{-}NH_2$ ; it makes amino acids amphoteric (acting as acid via $\text{-}NH_3^+$ and base via $\text{-}COO^-$ ).
Isoelectric point (pI): the pH at which the amino acid exists mainly as the zwitterion with zero net charge and shows no migration in an electric field.
A peptide bond is the amide ( $\text{-}CO\text{-}NH\text{-}$ ) linkage formed between the $\text{-}COOH$ of one amino acid and the $\text{-}NH_2$ of the next, with loss of water.
Essential amino acids cannot be synthesised by the body and must come from the diet (e.g. valine, leucine, lysine); non-essential ones the body can make itself.
Classification by side chain: acidic (extra $\text{-}COOH$ , e.g. aspartic/glutamic acid), basic (extra $\text{-}NH_2$ , e.g. lysine), neutral (e.g. glycine, alanine).
Amino acids are high-melting crystalline solids, soluble in water but insoluble in non-polar solvents, because their zwitterionic (ionic, salt-like) nature gives strong electrostatic lattice forces.
In acidic solution (pH below pI) the amino acid gains a proton and exists as the cation $H_3N^+\text{-}CHR\text{-}COOH$ ; in basic solution (pH above pI) it loses one to give the anion $H_2N\text{-}CHR\text{-}COO^-$ .
All $\alpha$ -amino acids except glycine are chiral and optically active; naturally occurring protein amino acids belong to the L-series.
Of the 20 standard amino acids about 10 are essential for humans; the rest are non-essential, and amino acids combine in any sequence to build proteins.
Dipeptides, tripeptides and polypeptides are named by the number of amino-acid residues joined by peptide bonds; a protein is a long polypeptide with a defined sequence.
By convention a peptide is written N-terminal (free $\text{-}NH_2$ ) on the left to C-terminal (free $\text{-}COOH$ ) on the right.

Where the marks go

Writing the zwitterion as overall charged — it is dipolar with zero NET charge (one $+$ and one $-$ ), which is why it does not migrate at the isoelectric point.
Calling glycine optically active — its $\alpha$ -carbon has two H atoms, so it is the one achiral standard amino acid.
Confusing the migration direction: below the $pI$ the amino acid is a cation and moves to the cathode; above the $pI$ it is an anion and moves to the anode.
Describing the peptide bond as an ester or simple C-N single bond — it is specifically an amide ( $\text{-}CO\text{-}NH\text{-}$ ) linkage formed with loss of water.
Equating 'essential' with 'more important' — essential just means the body cannot synthesise it, so it must come from diet.

How the board asks it

Define / statezwitterion, isoelectric point, peptide bond and essential amino acid definitions
Define the term isoelectric point. State the net charge on an $\alpha$ -amino acid at its isoelectric point and what this implies about its migration in an electric field.
Structure / naminggeneral $\alpha$ -amino acid, zwitterion and peptide-bond formation
Draw the structure of the zwitterion of glycine, and write the equation for the formation of a dipeptide from glycine and alanine, clearly marking the peptide bond.
Give reasonszwitterionic (ionic, salt-like) nature explaining physical properties
Account for the fact that $\alpha$ -amino acids are high-melting crystalline solids that are soluble in water but almost insoluble in non-polar solvents.
Predict the productcation and anion forms above and below the $pI$
Show, with structures, the form in which the $\alpha$ -amino acid $H_2N\text{-}CHR\text{-}COOH$ exists in (i) strongly acidic solution and (ii) strongly basic solution, and state the electrode towards which each form migrates.
Distinguishessential vs non-essential and acidic/basic/neutral classification
Distinguish between an essential and a non-essential amino acid, giving one example of each, and classify lysine as acidic, basic or neutral, giving a reason.
Assertion–Reasonchirality of $\alpha$ -amino acids with glycine as the achiral exception
Assertion: All $\alpha$ -amino acids found in proteins are optically active. Reason: Each $\alpha$ -amino acid has a chiral $\alpha$ -carbon bearing four different groups. State whether the assertion and reason are true, and whether the reason correctly explains the assertion.

Practise this topic

PreviousPolysaccharides: Starch, Cellulose & Glycogen NextProtein Structure & Denaturation

Written for Sublevo. Question text quoted anywhere in these notes is the Council’s and carries its year and paper; the board’s own diagrams are not reproduced.